\contentsline {chapter}{FIGURES}{iii}{chapter*.2}
\contentsline {chapter}{{CHAPTER\ 1: INTRO}}{1}{chapter.1}
\contentsline {section}{\numberline {1.1}Overview}{1}{section.1.1}
\contentsline {section}{\numberline {1.2}Bioinformatics Web Portals}{1}{section.1.2}
\contentsline {section}{\numberline {1.3}Bioinformatics Pipelines}{2}{section.1.3}
\contentsline {section}{\numberline {1.4}Rare Codon Analysis}{2}{section.1.4}
\contentsline {chapter}{{CHAPTER\ 2: BIOCOMPUTE: Principles and Architecture of a Bioinformatics Web Portal}}{3}{chapter.2}
\contentsline {section}{\numberline {2.1}Introduction}{3}{section.2.1}
\contentsline {section}{\numberline {2.2}System Goals}{4}{section.2.2}
\contentsline {section}{\numberline {2.3}Data-Action-Queue}{5}{section.2.3}
\contentsline {section}{\numberline {2.4}System Interface Implementation}{7}{section.2.4}
\contentsline {subsection}{\numberline {2.4.1}Data}{7}{subsection.2.4.1}
\contentsline {subsection}{\numberline {2.4.2}Action}{8}{subsection.2.4.2}
\contentsline {subsection}{\numberline {2.4.3}Queue}{9}{subsection.2.4.3}
\contentsline {subsection}{\numberline {2.4.4}System Description}{9}{subsection.2.4.4}
\contentsline {subsection}{\numberline {2.4.5}Biocompute Modules}{9}{subsection.2.4.5}
\contentsline {subsection}{\numberline {2.4.6}Sharing Work Across Machines}{12}{subsection.2.4.6}
\contentsline {subsubsection}{\numberline {2.4.6.1}Crawler}{12}{subsubsection.2.4.6.1}
\contentsline {subsubsection}{\numberline {2.4.6.2}Using Work-Queue's Catalog Server}{13}{subsubsection.2.4.6.2}
\contentsline {subsection}{\numberline {2.4.7}Data Management for BLAST}{13}{subsection.2.4.7}
\contentsline {subsection}{\numberline {2.4.8}Performance of Data Management Schemes}{15}{subsection.2.4.8}
\contentsline {subsection}{\numberline {2.4.9}Social Challenges of Biocompute}{17}{subsection.2.4.9}
\contentsline {section}{\numberline {2.5}Related Work}{18}{section.2.5}
\contentsline {section}{\numberline {2.6}Conclusions}{19}{section.2.6}
\contentsline {chapter}{{CHAPTER\ 3: Pipelines for Bioinformatics Computing}}{21}{chapter.3}
\contentsline {section}{\numberline {3.1}Introduction}{21}{section.3.1}
\contentsline {section}{\numberline {3.2}Microsatellite Pipeline}{21}{section.3.2}
\contentsline {subsection}{\numberline {3.2.1}Introduction}{21}{subsection.3.2.1}
\contentsline {subsection}{\numberline {3.2.2}Pipeline Description}{22}{subsection.3.2.2}
\contentsline {subsection}{\numberline {3.2.3}Performance}{22}{subsection.3.2.3}
\contentsline {section}{\numberline {3.3}Ka/Ks pipeline}{22}{section.3.3}
\contentsline {subsection}{\numberline {3.3.1}Introduction}{22}{subsection.3.3.1}
\contentsline {subsection}{\numberline {3.3.2}Pipeline Description}{22}{subsection.3.3.2}
\contentsline {subsection}{\numberline {3.3.3}Transcriptomics Challenges}{22}{subsection.3.3.3}
\contentsline {subsubsection}{\numberline {3.3.3.1}Existing Solutions}{23}{subsubsection.3.3.3.1}
\contentsline {subsubsection}{\numberline {3.3.3.2}Novel Solution}{23}{subsubsection.3.3.3.2}
\contentsline {subsubsection}{\numberline {3.3.3.3}Design}{24}{subsubsection.3.3.3.3}
\contentsline {subsubsection}{\numberline {3.3.3.4}Results}{24}{subsubsection.3.3.3.4}
\contentsline {subsection}{\numberline {3.3.4}Performance}{25}{subsection.3.3.4}
\contentsline {section}{\numberline {3.4}Practical Difficulties}{25}{section.3.4}
\contentsline {subsection}{\numberline {3.4.1}Evil Magic Numbers}{25}{subsection.3.4.1}
\contentsline {subsection}{\numberline {3.4.2}Encapsulation}{25}{subsection.3.4.2}
\contentsline {subsection}{\numberline {3.4.3}Lessons Learned}{25}{subsection.3.4.3}
\contentsline {chapter}{{CHAPTER\ 4: RARECODONS}}{26}{chapter.4}
\contentsline {section}{\numberline {4.1}Abstract}{26}{section.4.1}
\contentsline {section}{\numberline {4.2}Introduction}{26}{section.4.2}
\contentsline {section}{\numberline {4.3}Methods}{31}{section.4.3}
\contentsline {subsection}{\numberline {4.3.1}pre-processing}{31}{subsection.4.3.1}
\contentsline {subsection}{\numberline {4.3.2}Peak Method}{31}{subsection.4.3.2}
\contentsline {subsection}{\numberline {4.3.3}Poisson Sampling}{31}{subsection.4.3.3}
\contentsline {subsection}{\numberline {4.3.4}Limitation of Poisson}{31}{subsection.4.3.4}
\contentsline {subsection}{\numberline {4.3.5}Holistic Evaluation of Rare Codon Co-Occurrence}{34}{subsection.4.3.5}
\contentsline {subsection}{\numberline {4.3.6}Comparison Measures}{34}{subsection.4.3.6}
\contentsline {subsubsection}{\numberline {4.3.6.1}n99}{36}{subsubsection.4.3.6.1}
\contentsline {subsubsection}{\numberline {4.3.6.2}skew}{36}{subsubsection.4.3.6.2}
\contentsline {subsubsection}{\numberline {4.3.6.3}solomon}{36}{subsubsection.4.3.6.3}
\contentsline {subsubsection}{\numberline {4.3.6.4}kurtosis}{36}{subsubsection.4.3.6.4}
\contentsline {subsubsection}{\numberline {4.3.6.5}Correlation of Comparison Measures}{36}{subsubsection.4.3.6.5}
\contentsline {subsection}{\numberline {4.3.7}Controlling for GC-content}{37}{subsection.4.3.7}
\contentsline {subsection}{\numberline {4.3.8}Visualization}{37}{subsection.4.3.8}
\contentsline {section}{\numberline {4.4}Results}{37}{section.4.4}
\contentsline {subsection}{\numberline {4.4.1}Performance}{37}{subsection.4.4.1}
\contentsline {subsection}{\numberline {4.4.2}Biological Results}{37}{subsection.4.4.2}
\contentsline {chapter}{{CHAPTER\ 5: CONCLUSION AND FUTURE WORK}}{39}{chapter.5}
\contentsline {section}{\numberline {5.1}Future Work}{39}{section.5.1}
\contentsline {subsection}{\numberline {5.1.1}Improvements to Biocompute}{39}{subsection.5.1.1}
\contentsline {subsection}{\numberline {5.1.2}Future Rare Codon Work}{39}{subsection.5.1.2}
\contentsline {section}{\numberline {5.2}Conclusions}{39}{section.5.2}
\contentsline {chapter}{BIBLIOGRAPHY}{40}{chapter*.3}
